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Krypton in PDB 5o17: Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton

Protein crystallography data

The structure of Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton, PDB code: 5o17 was solved by N.Colloc'h, T.Prange, B.Vallone, P.Carpentier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 88.010, 88.010, 113.490, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 22

Other elements in 5o17:

The structure of Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton also contains other interesting chemical elements:

Iron (Fe) 1 atom

Krypton Binding Sites:

The binding sites of Krypton atom in the Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton (pdb code 5o17). This binding sites where shown within 5.0 Angstroms radius around Krypton atom.
In total 4 binding sites of Krypton where determined in the Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton, PDB code: 5o17:
Jump to Krypton binding site number: 1; 2; 3; 4;

Krypton binding site 1 out of 4 in 5o17

Go back to Krypton Binding Sites List in 5o17
Krypton binding site 1 out of 4 in the Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 1 of Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr204

b:25.4
occ:0.80
OG A:SER55 3.3 10.1 1.0
CD2 A:LEU56 3.5 15.7 1.0
N A:ALA29 3.6 7.2 1.0
CG A:LEU56 3.6 13.3 1.0
CD2 A:PHE32 3.6 8.2 1.0
CA A:ALA29 3.7 7.9 1.0
C A:PHE28 3.7 7.8 1.0
O A:PHE28 3.9 7.8 1.0
CE2 A:PHE32 3.9 8.3 1.0
CD1 A:LEU56 4.0 15.6 1.0
O A:PRO52 4.0 11.2 1.0
O A:HOH417 4.1 24.4 1.0
CB A:PHE28 4.1 9.0 1.0
CB A:ALA29 4.2 7.8 1.0
CE2 A:PHE61 4.3 10.4 1.0
CZ A:PHE61 4.5 10.5 1.0
CA A:PHE28 4.6 7.9 1.0
C A:PRO52 4.7 10.7 1.0
CB A:SER55 4.7 10.3 1.0
O A:THR25 4.7 9.9 1.0
CG A:PHE32 4.8 7.5 1.0
CB A:PRO52 4.8 13.0 1.0
O A:HOH338 4.9 14.5 1.0
C A:ALA29 5.0 7.5 1.0

Krypton binding site 2 out of 4 in 5o17

Go back to Krypton Binding Sites List in 5o17
Krypton binding site 2 out of 4 in the Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 2 of Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr205

b:30.8
occ:1.00
CG A:LEU136 3.9 25.0 1.0
CA A:TYR137 3.9 17.5 1.0
CZ3 A:TRP133 4.0 16.8 1.0
N A:TYR137 4.0 20.2 1.0
CD2 A:LEU136 4.1 25.1 1.0
CG2 A:ILE72 4.1 16.8 1.0
CD1 A:TYR137 4.1 17.4 1.0
CG2 A:VAL140 4.1 19.2 1.0
CB A:TYR137 4.2 16.9 1.0
CD2 A:LEU113 4.2 15.3 1.0
CE3 A:TRP133 4.3 16.5 1.0
C A:LEU136 4.4 22.7 1.0
CB A:ALA75 4.4 25.1 1.0
O A:LEU136 4.5 21.3 1.0
CG1 A:ILE72 4.5 16.8 1.0
CB A:LEU136 4.7 23.7 1.0
CG A:TYR137 4.7 17.3 1.0
CB A:ILE72 4.7 16.2 1.0
CB A:VAL140 4.8 19.4 1.0
CA A:ILE72 4.8 16.7 1.0
CD1 A:LEU136 4.8 26.4 1.0

Krypton binding site 3 out of 4 in 5o17

Go back to Krypton Binding Sites List in 5o17
Krypton binding site 3 out of 4 in the Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 3 of Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr206

b:33.4
occ:0.35
CG1 A:VAL109 3.5 13.5 1.0
CD1 A:ILE72 3.6 19.0 1.0
CE1 A:TYR137 3.7 17.5 1.0
CMC A:HEM201 3.9 19.7 1.0
CG1 A:ILE72 4.1 16.8 1.0
CG1 A:VAL68 4.1 14.2 1.0
CD1 A:LEU27 4.2 10.7 1.0
CD2 A:LEU113 4.2 15.3 1.0
CBC A:HEM201 4.3 20.9 1.0
CD1 A:TYR137 4.3 17.4 1.0
CB A:LEU113 4.4 12.8 1.0
CZ A:TYR137 4.6 17.2 1.0
CG A:LEU113 4.7 14.7 1.0
OH A:TYR137 4.7 17.9 1.0
O A:VAL109 4.8 10.4 1.0
CD1 A:LEU113 4.8 15.5 1.0
CB A:VAL109 5.0 12.1 1.0

Krypton binding site 4 out of 4 in 5o17

Go back to Krypton Binding Sites List in 5o17
Krypton binding site 4 out of 4 in the Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 4 of Crystal Structure of Murine Neuroglobin Under 100 Bar Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Kr210

b:34.2
occ:0.20
CB A:TYR137 3.1 16.9 1.0
O A:HOH409 3.3 35.7 1.0
CG A:LEU114 3.5 17.7 1.0
CG A:TYR137 3.5 17.3 1.0
O A:GLY110 3.6 10.5 1.0
CD2 A:LEU114 3.6 19.1 1.0
O A:TRP133 3.7 22.4 1.0
CD2 A:TYR137 3.8 17.3 1.0
CA A:SER134 4.0 21.1 1.0
CD1 A:LEU114 4.0 21.4 1.0
CA A:GLY110 4.0 10.5 1.0
C A:TRP133 4.1 21.0 1.0
CD2 A:LEU113 4.1 15.3 1.0
C A:GLY110 4.1 10.3 1.0
N A:SER134 4.2 21.1 1.0
O A:HOH376 4.4 38.3 1.0
CD1 A:TYR137 4.4 17.4 1.0
CG A:LEU113 4.5 14.7 1.0
CA A:TYR137 4.6 17.5 1.0
CB A:LEU113 4.6 12.8 1.0
CE2 A:TYR137 4.7 17.3 1.0
CB A:LEU114 4.8 15.6 1.0
O A:SER134 4.8 19.8 1.0
N A:LEU114 4.8 11.9 1.0
CB A:SER134 4.8 23.0 1.0
C A:SER134 4.8 21.4 1.0
CB A:TRP133 4.9 19.9 1.0
N A:TYR137 4.9 20.2 1.0

Reference:

N.Colloc'h, P.Carpentier, L.C.Montemiglio, B.Vallone, T.Prange. Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas Under Pressure. Biophys. J. V. 113 2199 2017.
ISSN: ESSN 1542-0086
PubMed: 29108649
DOI: 10.1016/J.BPJ.2017.10.014
Page generated: Mon Dec 14 02:54:47 2020

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